{"id":"https://openalex.org/W2152302868","doi":"https://doi.org/10.1093/bib/bbt077","title":"Investigating biocomplexity through the agent-based paradigm","display_name":"Investigating biocomplexity through the agent-based paradigm","publication_year":2013,"publication_date":"2013-11-12","ids":{"openalex":"https://openalex.org/W2152302868","doi":"https://doi.org/10.1093/bib/bbt077","mag":"2152302868","pmid":"https://pubmed.ncbi.nlm.nih.gov/24227161"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt077","pdf_url":"https://academic.oup.com/bib/article-pdf/16/1/137/5030642/bbt077.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/16/1/137/5030642/bbt077.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081032347","display_name":"Himanshu Kaul","orcid":"https://orcid.org/0000-0003-1586-7486"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H. Kaul","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5084823710","display_name":"Yiannis Ventikos","orcid":"https://orcid.org/0000-0002-8589-8117"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Y. Ventikos","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.7954,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.85184806,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"137","last_page":"152"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9822999835014343,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7319881319999695},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.545481264591217},{"id":"https://openalex.org/keywords/living-systems","display_name":"Living systems","score":0.5289461612701416},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4772112965583801},{"id":"https://openalex.org/keywords/turing","display_name":"Turing","score":0.4717705249786377},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4707750976085663},{"id":"https://openalex.org/keywords/dynamism","display_name":"Dynamism","score":0.4569951891899109},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4213750958442688},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37732556462287903},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.34922513365745544}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7319881319999695},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.545481264591217},{"id":"https://openalex.org/C2776184637","wikidata":"https://www.wikidata.org/wiki/Q6506039","display_name":"Living systems","level":2,"score":0.5289461612701416},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4772112965583801},{"id":"https://openalex.org/C9870796","wikidata":"https://www.wikidata.org/wiki/Q490481","display_name":"Turing","level":2,"score":0.4717705249786377},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4707750976085663},{"id":"https://openalex.org/C2775836275","wikidata":"https://www.wikidata.org/wiki/Q3502310","display_name":"Dynamism","level":2,"score":0.4569951891899109},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4213750958442688},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37732556462287903},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.34922513365745544},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt077","pdf_url":"https://academic.oup.com/bib/article-pdf/16/1/137/5030642/bbt077.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24227161","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24227161","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1465440","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1465440/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   Brief Bioinform , 16  (1)   137 - 152.   (2015)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4293376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4293376","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt077","pdf_url":"https://academic.oup.com/bib/article-pdf/16/1/137/5030642/bbt077.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152302868.pdf"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W13406669","https://openalex.org/W54348722","https://openalex.org/W121819372","https://openalex.org/W1496074117","https://openalex.org/W1511064218","https://openalex.org/W1539819149","https://openalex.org/W1570009092","https://openalex.org/W1578276312","https://openalex.org/W1597041602","https://openalex.org/W1768149473","https://openalex.org/W1849361375","https://openalex.org/W1971441460","https://openalex.org/W1974034376","https://openalex.org/W1975658784","https://openalex.org/W1977523316","https://openalex.org/W1977578104","https://openalex.org/W1977608305","https://openalex.org/W1981477992","https://openalex.org/W1982376793","https://openalex.org/W1984976654","https://openalex.org/W1985032931","https://openalex.org/W1987404075","https://openalex.org/W1988780658","https://openalex.org/W1989301826","https://openalex.org/W1989393824","https://openalex.org/W1990574061","https://openalex.org/W1996021286","https://openalex.org/W1996449803","https://openalex.org/W2000993713","https://openalex.org/W2002785668","https://openalex.org/W2004929506","https://openalex.org/W2010253407","https://openalex.org/W2011551706","https://openalex.org/W2013141236","https://openalex.org/W2014520808","https://openalex.org/W2014781793","https://openalex.org/W2017853518","https://openalex.org/W2019066182","https://openalex.org/W2019216430","https://openalex.org/W2021731136","https://openalex.org/W2024771744","https://openalex.org/W2029834210","https://openalex.org/W2033582549","https://openalex.org/W2034269086","https://openalex.org/W2038785086","https://openalex.org/W2039167655","https://openalex.org/W2044910634","https://openalex.org/W2046314718","https://openalex.org/W2052098523","https://openalex.org/W2053157043","https://openalex.org/W2058943257","https://openalex.org/W2060252860","https://openalex.org/W2065192198","https://openalex.org/W2067527568","https://openalex.org/W2068366994","https://openalex.org/W2070431772","https://openalex.org/W2075052929","https://openalex.org/W2080130042","https://openalex.org/W2086705790","https://openalex.org/W2089072707","https://openalex.org/W2091413795","https://openalex.org/W2096352448","https://openalex.org/W2099190885","https://openalex.org/W2101235176","https://openalex.org/W2103093087","https://openalex.org/W2103337096","https://openalex.org/W2104154419","https://openalex.org/W2105656578","https://openalex.org/W2105850748","https://openalex.org/W2110937552","https://openalex.org/W2112036221","https://openalex.org/W2112682311","https://openalex.org/W2112979244","https://openalex.org/W2114390083","https://openalex.org/W2114888488","https://openalex.org/W2114952275","https://openalex.org/W2115736286","https://openalex.org/W2119189484","https://openalex.org/W2124457330","https://openalex.org/W2124677924","https://openalex.org/W2126160338","https://openalex.org/W2127062858","https://openalex.org/W2129367983","https://openalex.org/W2130201056","https://openalex.org/W2132699577","https://openalex.org/W2140533119","https://openalex.org/W2141890333","https://openalex.org/W2144954160","https://openalex.org/W2150704630","https://openalex.org/W2152734262","https://openalex.org/W2154718031","https://openalex.org/W2155272711","https://openalex.org/W2156571897","https://openalex.org/W2157999920","https://openalex.org/W2158130697","https://openalex.org/W2165620349","https://openalex.org/W2168414272","https://openalex.org/W2168967248","https://openalex.org/W2171151276","https://openalex.org/W2238191081","https://openalex.org/W2483106842","https://openalex.org/W2493960853","https://openalex.org/W2495019760","https://openalex.org/W2499582061","https://openalex.org/W2986348978","https://openalex.org/W3128894147","https://openalex.org/W4256246874","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2000438032","https://openalex.org/W2775384662","https://openalex.org/W2385556862","https://openalex.org/W4297802007","https://openalex.org/W2117883229","https://openalex.org/W2367908682","https://openalex.org/W2586399084","https://openalex.org/W4231710131","https://openalex.org/W4232893935","https://openalex.org/W109426479"],"abstract_inverted_index":{"Capturing":[0],"the":[1,15,19,25,39,56,86,102,133,142,150,189,228,234],"dynamism":[2],"that":[3,11,44,122,230,242],"pervades":[4],"biological":[5,92,197,210,217,240],"systems":[6,79,93,241],"requires":[7],"a":[8,35,95,116,138,213],"computational":[9,120,176],"approach":[10,237],"can":[12],"accommodate":[13],"both":[14],"continuous":[16],"features":[17],"of":[18,30,64,90,97,118,137,180,195,216],"system":[20,50,151],"environment":[21],"as":[22,24],"well":[23],"flexible":[26],"and":[27,88,192,247],"heterogeneous":[28,83],"nature":[29],"component":[31,46],"interactions.":[32],"This":[33],"presents":[34],"serious":[36],"challenge":[37],"for":[38],"more":[40],"traditional":[41],"mathematical":[42,53],"approaches":[43,121],"assume":[45],"homogeneity":[47,57],"to":[48,62,72,78,149,162,172,208,221,238,244],"relate":[49],"observables":[51],"using":[52],"equations.":[54],"While":[55],"condition":[58],"does":[59],"not":[60],"lead":[61],"loss":[63],"accuracy":[65],"while":[66],"simulating":[67],"various":[68],"continua,":[69],"it":[70],"fails":[71],"offer":[73,108,146],"detailed":[74],"solutions":[75],"when":[76],"applied":[77],"with":[80,174,184],"dynamically":[81],"interacting":[82],"components.":[84],"As":[85],"functionality":[87],"architecture":[89],"most":[91,190,235],"is":[94,115,187],"product":[96],"multi-faceted":[98],"individual":[99],"interactions":[100,125],"at":[101],"sub-system":[103],"level,":[104],"continuum":[105,159,185],"models":[106,186],"rarely":[107],"much":[109],"beyond":[110],"qualitative":[111],"similarity.":[112],"Agent-based":[113],"modelling":[114,204,233],"class":[117],"algorithmic":[119],"rely":[123],"on":[124],"between":[126],"Turing-complete":[127],"finite-state":[128],"machines--or":[129],"agents--to":[130],"simulate,":[131],"from":[132],"bottom-up,":[134],"macroscopic":[135],"properties":[136],"system.":[139],"In":[140,223],"recognizing":[141],"heterogeneity":[143],"condition,":[144],"they":[145,168],"suitable":[147],"ontologies":[148],"components":[152],"being":[153,165],"modelled,":[154],"thereby":[155],"succeeding":[156],"where":[157],"their":[158],"counterparts":[160],"tend":[161,243],"struggle.":[163],"Furthermore,":[164],"inherently":[166],"hierarchical,":[167],"are":[169],"quite":[170],"amenable":[171],"coupling":[173],"other":[175],"paradigms.":[177],"The":[178],"integration":[179],"any":[181],"agent-based":[182,203,232],"framework":[183],"arguably":[188],"elegant":[191],"precise":[193,236],"way":[194],"representing":[196],"systems.":[198],"Although":[199],"in":[200],"its":[201],"nascence,":[202],"has":[205],"been":[206],"utilized":[207],"model":[209,239],"complexity":[211],"across":[212],"broad":[214],"range":[215],"scales":[218],"(from":[219],"cells":[220],"societies).":[222],"this":[224],"article,":[225],"we":[226],"explore":[227],"reasons":[229],"make":[231],"be":[245],"non-linear":[246],"complex.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":11},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}